Hi Anastasia,
Yes. I tried to run bedpostx on a stand-alone computer but it is very
slow although it can work well.
Regarding the b-values, we do have some subjects which were scanned in
different protocols a few years ago. If it is possible, please add the
option to the new version of Tracula, or it's even better to let me know
how can I change the script by myself.
I have updated the new version of freesurfer, so, I don't need to use
nb0 variable anymore. Thanks for your reminder.
Best,
Xiaofu
Best,
Xiaofu
On Wed, May 27, 2015 at 12:20 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Xiaofu - As I said earlier, it is impossible for us to troubleshoot
> problems with every single type of cluster, especially a type we don't
> have. You'll have to troubleshoot it with your cluster admin, or try to run
> bedpostx on a stand-alone computer. About your other questions:
>
> 1. Currently there is no option to have a different set of b-values for
> each subject. Are you using a different scanning protocol for different
> subjects?
>
> 2. The fact that you mention the nb0 variable tells me that you don't have
> the latest version of freesurfer. It is highly recommended that you run
> tracula from the 5.3 version of freesurfer, after also downloading the
> tracula update posted here:
> http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
> In the newer version, there is no nb0 variable, the program figures it out
> from the b-value file. But again, it is not ideal to have a different
> number of b=0 images for each subject.
>
> Best,
> a.y
>
>
> On Tue, 26 May 2015, Xiaofu wrote:
>
> Dear Anastasia,
>> Thanks for your answer. I tried to replace 'bedpostx_mgh' with
>> 'bedpostx'
>> in the shell file 'tract-all' in order to run Tracula in the C2B2 server
>> (Titan cluster). But it failed as well. Is there anyway to run Tracula,
>> i.e., by pass the running error of bedpostx_mgh?
>> Besides, I have two more questions when I set up a configuration file.
>> 1) In the step9 of Tracula tutorial
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), i.e.,
>> Specify the b-value table, I can only set bvalfile to specify the location
>> of the b-value table. Can I specify a different b value file for each of
>> the
>> scans in the study (with bvallist,for example) besides a single b value
>> file
>> for all scans in the study (with bvalfile).
>> 2) About the number of low-b images.
>> Since I will use 4D nifty images instead of raw DICOMs, I need to set
>> the number of low-b images in the configuration file, i.e., set nb0. Can
>> I
>> specify a different nb0 value for each of the scans in the study (with
>> nb0list,for example) besides a single nb0 value for all scans in the
>> study.
>>
>> Best,
>> Xiaofu
>>
>> On Fri, May 22, 2015 at 1:35 PM, Anastasia Yendiki
>> <ayend...@nmr.mgh.harvard.edu> wrote:
>>
>> Hi Xiaofu - The bedpostx program is not configured to run on any
>> type of cluster with any type of queueing software. It was
>> originally written to be run on an SGE cluster with specific
>> queue names. The bedpostx_mgh is a modified version that also
>> works on our PBS cluster. Making it work on additional clusters
>> would require additional tweaks, and it's impossible for us to
>> make it work on everyone's cluster.
>>
>> In a future version, I'd like to give the option to simply print
>> out all the necessary commands, and then it would be up to the
>> user to figure out how to submit them as jobs on their own
>> cluster. This is not implemented yet.
>>
>> a.y
>>
>> On Tue, 19 May 2015, Xiaofu wrote:
>>
>> Dear Sir/Madam, I tried to run Tracula in the C2B2
>> server at Columbia University. However, I got the
>> following error message
>> after submitted my job using qsub to the sever. I'd
>> greatly appreciate it if you could help me resolve
>> this problem.
>>
>> WARN: Running FSL's bedbost locally - this might
>> take a while
>> WARN: It is recommended to run this step on a
>> cluster
>> bedpostx_mgh -n 2 /DTIdata/Tracula/3789/dmri
>> subjectdir is /DTIdata/Tracula/3789/dmri
>> Making bedpostx directory structure
>> Queuing preprocessing stages
>> Unable to run job: Job was rejected because job
>> requests unknown queue "short.q".
>> Exiting.
>> Queuing parallel processing stage
>> Unable to run job: Job was rejected because job
>> requests unknown queue "long.q".
>> Exiting.
>> Queuing post processing stage
>> Unable to run job: Job was rejected because job
>> requests unknown queue "long.q".
>> Exiting.
>>
>> Looking forward to hearing from you. Thank you very
>> much.
>>
>>
>> Best,
>>
>> Xiaofu
>>
>>
>>
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